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Omrani M, Beyrampour-Basmenj H, Jahanban-Esfahlan R, Talebi M, Raeisi M, Serej ZA, Akbar-Gharalari N, Khodakarimi S, Wu J, Ebrahimi-Kalan A. Global trend in exosome isolation and application: an update concept in management of diseases. Mol Cell Biochem 2024; 479:679-691. [PMID: 37166542 PMCID: PMC10173230 DOI: 10.1007/s11010-023-04756-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/28/2023] [Indexed: 05/12/2023]
Abstract
Extracellular vesicles (EVs) secreted by various cells offer great potential for use in the diagnosis and treatment of disease. EVs are heterogeneous membranous vesicles. Exosomes are a subtype of EVs, 40-150 nm spherical vesicles with a lipid layer derived from endosomes. Exosomes, which are involved in signal transduction and maintain homeostasis, are released from almost all cells, tissues, and body fluids. Although several methods exist to isolate and characterize EVs and exosomes, each technique has significant drawbacks and limitations that prevent progress in the field. New approaches in the biology of EVs show great potential for isolating and characterizing EVs, which will help us better understand their biological function. The strengths and limitations of conventional strategies and novel methods (microfluidic) for EV isolation are outlined in this review. We also present various exosome isolation techniques and kits that are commercially available and assess the global market demand for exosome assays.
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Affiliation(s)
- Mohammadhassan Omrani
- Department of Neurosciences and Cognition, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hanieh Beyrampour-Basmenj
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahnaz Talebi
- Department of Neurosciences and Cognition, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mortaza Raeisi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zeinab Aliyari Serej
- Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Naeimeh Akbar-Gharalari
- Department of Neurosciences and Cognition, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sina Khodakarimi
- Department of Neurosciences and Cognition, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jiaqian Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, 77030, USA.
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Abbas Ebrahimi-Kalan
- Department of Neurosciences and Cognition, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
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Sandau US, Magaña SM, Costa J, Nolan JP, Ikezu T, Vella LJ, Jackson HK, Moreira LR, Palacio PL, Hill AF, Quinn JF, Van Keuren‐Jensen KR, McFarland TJ, Palade J, Sribnick EA, Su H, Vekrellis K, Coyle B, Yang Y, Falcón‐Perez JM, Nieuwland R, Saugstad JA. Recommendations for reproducibility of cerebrospinal fluid extracellular vesicle studies. J Extracell Vesicles 2024; 13:e12397. [PMID: 38158550 PMCID: PMC10756860 DOI: 10.1002/jev2.12397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/09/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024] Open
Abstract
Cerebrospinal fluid (CSF) is a clear, transparent fluid derived from blood plasma that protects the brain and spinal cord against mechanical shock, provides buoyancy, clears metabolic waste and transports extracellular components to remote sites in the brain. Given its contact with the brain and the spinal cord, CSF is the most informative biofluid for studies of the central nervous system (CNS). In addition to other components, CSF contains extracellular vesicles (EVs) that carry bioactive cargoes (e.g., lipids, nucleic acids, proteins), and that can have biological functions within and beyond the CNS. Thus, CSF EVs likely serve as both mediators of and contributors to communication in the CNS. Accordingly, their potential as biomarkers for CNS diseases has stimulated much excitement for and attention to CSF EV research. However, studies on CSF EVs present unique challenges relative to EV studies in other biofluids, including the invasive nature of CSF collection, limited CSF volumes and the low numbers of EVs in CSF as compared to plasma. Here, the objectives of the International Society for Extracellular Vesicles CSF Task Force are to promote the reproducibility of CSF EV studies by providing current reporting and best practices, and recommendations and reporting guidelines, for CSF EV studies. To accomplish this, we created and distributed a world-wide survey to ISEV members to assess methods considered 'best practices' for CSF EVs, then performed a detailed literature review for CSF EV publications that was used to curate methods and resources. Based on responses to the survey and curated information from publications, the CSF Task Force herein provides recommendations and reporting guidelines to promote the reproducibility of CSF EV studies in seven domains: (i) CSF Collection, Processing, and Storage; (ii) CSF EV Separation/Concentration; (iii) CSF EV Size and Number Measurements; (iv) CSF EV Protein Studies; (v) CSF EV RNA Studies; (vi) CSF EV Omics Studies and (vii) CSF EV Functional Studies.
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Affiliation(s)
- Ursula S. Sandau
- Department of Anesthesiology & Perioperative MedicineOregon Health & Science UniversityPortlandOregonUSA
| | - Setty M. Magaña
- Center for Clinical and Translational Research, Abigail Wexner Research InstituteNationwide Children's HospitalColumbusOhioUSA
| | - Júlia Costa
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de Lisboa, Avenida da RepúblicaOeirasPortugal
| | - John P. Nolan
- Scintillon Institute for Biomedical and Bioenergy ResearchSan DiegoCaliforniaUSA
| | - Tsuneya Ikezu
- Department of NeuroscienceMayo Clinic FloridaJacksonvilleFloridaUSA
| | - Laura J. Vella
- Department of Surgery, The Royal Melbourne HospitalThe University of MelbourneParkvilleVictoriaAustralia
- The Florey Institute of Neuroscience and Mental HealthUniversity of MelbourneParkville, MelbourneVictoriaAustralia
| | - Hannah K. Jackson
- Department of PathologyUniversity of CambridgeCambridgeUK
- Exosis, Inc.Palm BeachFloridaUSA
| | - Lissette Retana Moreira
- Department of Parasitology, Faculty of MicrobiologyUniversity of Costa RicaSan JoséCosta Rica, Central America
- Centro de Investigación en Enfermedades TropicalesUniversity of Costa RicaSan JoséCosta Rica, Central America
| | - Paola Loreto Palacio
- Center for Clinical and Translational Research, Abigail Wexner Research InstituteNationwide Children's HospitalColumbusOhioUSA
| | - Andrew F. Hill
- Institute for Health and SportVictoria UniversityMelbourneVictoriaAustralia
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Joseph F. Quinn
- Department of NeurologyOregon Health & Science UniversityPortlandOregonUSA
- Portland VA Medical CenterPortlandOregonUSA
| | | | - Trevor J. McFarland
- Department of Anesthesiology & Perioperative MedicineOregon Health & Science UniversityPortlandOregonUSA
| | - Joanna Palade
- Neurogenomics DivisionTranslational Genomics Research InstitutePhoenixArizonaUSA
| | - Eric A. Sribnick
- Department of NeurosurgeryNationwide Children's Hospital, The Ohio State UniversityColumbusOhioUSA
| | - Huaqi Su
- The Florey Institute of Neuroscience and Mental HealthUniversity of MelbourneParkville, MelbourneVictoriaAustralia
| | | | - Beth Coyle
- Children's Brain Tumour Research Centre, School of MedicineUniversity of Nottingham Biodiscovery Institute, University of NottinghamNottinghamNottinghamshireUK
| | - You Yang
- Scintillon Institute for Biomedical and Bioenergy ResearchSan DiegoCaliforniaUSA
| | - Juan M. Falcón‐Perez
- Exosomes Laboratory, Center for Cooperative Research in BiosciencesBasque Research and Technology AllianceDerioSpain
- Metabolomics Platform, Center for Cooperative Research in BiosciencesBasque Research and Technology AllianceDerioSpain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y DigestivasMadridSpain
- Ikerbasque, Basque Foundation for ScienceBilbaoSpain
| | - Rienk Nieuwland
- Laboratory of Experimental Clinical Chemistry, Amsterdam University Medical Centers, Location AMCUniversity of AmsterdamAmsterdamThe Netherlands
- Amsterdam Vesicle Center, Amsterdam University Medical Centers, Location AMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Julie A. Saugstad
- Department of Anesthesiology & Perioperative MedicineOregon Health & Science UniversityPortlandOregonUSA
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3
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Masaki K, Ahmed ABF, Ishida T, Mikami Y, Funabashi H, Hirota R, Ikeda T, Kuroda A. Chromatographic purification of small extracellular vesicles using an affinity column for phospholipid membranes. Biotechnol Lett 2023; 45:1457-1466. [PMID: 37787831 PMCID: PMC10635940 DOI: 10.1007/s10529-023-03430-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/01/2023] [Accepted: 08/17/2023] [Indexed: 10/04/2023]
Abstract
OBJECTIVES This study aimed to investigate whether chromatography using an ExoPUA column, an affinity column for phospholipid membranes, could potentially serve as an efficient, rapid, scalable, and reproducible method for purifying small extracellular vesicles (sEVs). RESULTS We used the ExoPUA column connected to a fast-performance liquid chromatography system. One-step chromatographic purification of sEVs from culture supernatant using the ExoPUA protocol resulted in an 82 ± 16-fold increase in purity with a yield of 38 ± 5% of sEVs. The purified sEVs contained CD9, CD63, TSG101, and miRNA (miR-21), but not the endoplasmic reticulum protein Calnexin. Transmission electron microscopy indicated that the purified sEVs were intact. The purification performance of the ExoPUA protocol showed superior results in terms of yield compared to that of the differential ultracentrifugation method, the most commonly used method for purifying sEVs in laboratories, and purity compared to that of the DEAE chromatography protocol. CONCLUSION The sEVs were effectively purified in the bind-elute mode and the ExoPUA column can be refreshed and sterilized with sodium hydroxide (NaOH), having high potential for multiple sEV purification in a scalable and industrial manner.
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Affiliation(s)
- Kanako Masaki
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Abo Bakr F Ahmed
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - Takenori Ishida
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Yuuki Mikami
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Hisakage Funabashi
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Ryuichi Hirota
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Takeshi Ikeda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8530, Japan.
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4
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Leggio L, Paternò G, Vivarelli S, Bonasera A, Pignataro B, Iraci N, Arrabito G. Label-free approaches for extracellular vesicle detection. iScience 2023; 26:108105. [PMID: 37867957 PMCID: PMC10589885 DOI: 10.1016/j.isci.2023.108105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023] Open
Abstract
Extracellular vesicles (EVs) represent pivotal mediators in cell-to-cell communication. They are lipid-membranous carriers of several biomolecules, which can be produced by almost all cells. In the current Era of precision medicine, EVs gained growing attention thanks to their potential in both biomarker discovery and nanotherapeutics applications. However, current technical limitations in isolating and/or detecting EVs restrain their standard use in clinics. This review explores all the state-of-the-art analytical technologies which are currently overcoming these issues. On one end, several innovative optical-, electrical-, and spectroscopy-based detection methods represent advantageous label-free methodologies for faster EV detection. On the other end, microfluidics-based lab-on-a-chip tools support EV purification from low-concentrated samples. Altogether, these technologies will strengthen the routine application of EVs in clinics.
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Affiliation(s)
- Loredana Leggio
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Greta Paternò
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Silvia Vivarelli
- Department of Biomedical and Dental Sciences, Morphological and Functional Imaging, Section of Occupational Medicine, University of Messina, Messina, Italy
| | - Aurelio Bonasera
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, building 17, 90128 Palermo, Italy
| | - Bruno Pignataro
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, building 17, 90128 Palermo, Italy
| | - Nunzio Iraci
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Giuseppe Arrabito
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, building 17, 90128 Palermo, Italy
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Sjoqvist S, Otake K. Saliva and Saliva Extracellular Vesicles for Biomarker Candidate Identification—Assay Development and Pilot Study in Amyotrophic Lateral Sclerosis. Int J Mol Sci 2023; 24:ijms24065237. [PMID: 36982312 PMCID: PMC10049503 DOI: 10.3390/ijms24065237] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023] Open
Abstract
Saliva is gaining increasing attention as a source of biomarkers due to non-invasive and undemanding collection access. Extracellular vesicles (EVs) are nano-sized, cell-released particles that contain molecular information about their parent cells. In this study, we developed methods for saliva biomarker candidate identification using EV-isolation and proteomic evaluation. We used pooled saliva samples for assay development. EVs were isolated using membrane affinity-based methods followed by their characterization using nanoparticle tracking analysis and transmission electron microscopy. Subsequently, both saliva and saliva-EVs were successfully analyzed using proximity extension assay and label-free quantitative proteomics. Saliva-EVs had a higher purity than plasma-EVs, based on the expression of EV-proteins and albumin. The developed methods could be used for the analysis of individual saliva samples from amyotrophic lateral sclerosis (ALS) patients and controls (n = 10 each). The starting volume ranged from 2.1 to 4.9 mL and the amount of total isolated EV-proteins ranged from 5.1 to 42.6 µg. Although no proteins were significantly differentially expressed between the two groups, there was a trend for a downregulation of ZNF428 in ALS-saliva-EVs and an upregulation of IGLL1 in ALS saliva. In conclusion, we have developed a robust workflow for saliva and saliva-EV analysis and demonstrated its technical feasibility for biomarker discovery.
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6
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A review on comparative studies addressing exosome isolation methods from body fluids. Anal Bioanal Chem 2023; 415:1239-1263. [PMID: 35838769 DOI: 10.1007/s00216-022-04174-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/17/2022] [Accepted: 06/10/2022] [Indexed: 12/11/2022]
Abstract
Exosomes emerged as valuable sources of disease biomarkers and new therapeutic tools. However, extracellular vesicles isolation with exosome-like characteristics from certain biofluids is still challenging which can limit their potential use in clinical settings. While ultracentrifugation-based procedures are the gold standard for exosome isolation from cell cultures, no unique and standardized method for exosome isolation from distinct body fluids exists. The complexity, specific composition, and physical properties of each biofluid constitute a technical barrier to obtain reproducible and pure exosome preparations, demanding a detailed characterization of both exosome isolation and characterization methods. Moreover, some isolation procedures can affect downstream proteomic or RNA profiling analysis. This review compiles and discussed a set of comparative studies addressing distinct exosome isolation methods from human biofluids, including cerebrospinal fluid, plasma, serum, saliva, and urine, also focusing on body fluid specific challenges, physical properties, and other potential variation sources. This summarized information will facilitate the choice of exosome isolation methods, based on the type of biological samples available, and hopefully encourage the use of exosomes in translational and clinical research.
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7
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Musatova OE, Rubtsov YP. Effects of glioblastoma-derived extracellular vesicles on the functions of immune cells. Front Cell Dev Biol 2023; 11:1060000. [PMID: 36960410 PMCID: PMC10028257 DOI: 10.3389/fcell.2023.1060000] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 02/22/2023] [Indexed: 03/09/2023] Open
Abstract
Glioblastoma is the most aggressive variant of glioma, the tumor of glial origin which accounts for 80% of brain tumors. Glioblastoma is characterized by astoundingly poor prognosis for patients; a combination of surgery, chemo- and radiotherapy used for clinical treatment of glioblastoma almost inevitably results in rapid relapse and development of more aggressive and therapy resistant tumor. Recently, it was demonstrated that extracellular vesicles produced by glioblastoma (GBM-EVs) during apoptotic cell death can bind to surrounding cells and change their phenotype to more aggressive. GBM-EVs participate also in establishment of immune suppressive microenvironment that protects glioblastoma from antigen-specific recognition and killing by T cells. In this review, we collected present data concerning characterization of GBM-EVs and study of their effects on different populations of the immune cells (T cells, macrophages, dendritic cells, myeloid-derived suppressor cells). We aimed at critical analysis of experimental evidence in order to conclude whether glioblastoma-derived extracellular vesicles are a major factor in immune evasion of this deadly tumor. We summarized data concerning potential use of GBM-EVs for non-invasive diagnostics of glioblastoma. Finally, the applicability of approaches aimed at blocking of GBM-EVs production or their fusion with target cells for treatment of glioblastoma was analyzed.
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Affiliation(s)
- Oxana E. Musatova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
| | - Yury P. Rubtsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
- N.N.Blokhin Russian Cancer Research Center, Ministry of Health of the Russian Federation, Moscow, Russia
- *Correspondence: Yury P. Rubtsov,
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8
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Assessment of Small Cellular Particles from Four Different Natural Sources and Liposomes by Interferometric Light Microscopy. Int J Mol Sci 2022; 23:ijms232415801. [PMID: 36555442 PMCID: PMC9779747 DOI: 10.3390/ijms232415801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/28/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
Small particles in natural sources are a subject of interest for their potential role in intercellular, inter-organism, and inter-species interactions, but their harvesting and assessment present a challenge due to their small size and transient identity. We applied a recently developed interferometric light microscopy (ILM) to assess the number density and hydrodynamic radius (Rh) of isolated small cellular particles (SCPs) from blood preparations (plasma and washed erythrocytes) (B), spruce needle homogenate (S), suspension of flagellae of microalgae Tetraselmis chuii (T), conditioned culture media of microalgae Phaeodactylum tricornutum (P), and liposomes (L). The aliquots were also assessed by flow cytometry (FCM), dynamic light scattering (DLS), ultraviolet-visible spectrometry (UV-vis), and imaging by cryogenic transmission electron microscopy (cryo-TEM). In Rh, ILM showed agreement with DLS within the measurement error in 10 out of 13 samples and was the only method used here that yielded particle density. Cryo-TEM revealed that representative SCPs from Tetraselmis chuii flagella (T) did not have a globular shape, so the interpretation by Rh of the batch methods was biased. Cryo-TEM showed the presence of thin filaments in isolates from Phaeodactylum tricornutum conditioned culture media (P), which provides an explanation for the considerably larger Rh obtained by batch methods than the sizes of particles observed by cryo-TEM images. ILM proved convenient for assessment of number density and Rh of SCPs in blood preparations (e.g., plasma); therefore, its use in population and clinical studies is indicated.
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9
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Fordjour FK, Guo C, Ai Y, Daaboul GG, Gould SJ. A shared, stochastic pathway mediates exosome protein budding along plasma and endosome membranes. J Biol Chem 2022; 298:102394. [PMID: 35988652 PMCID: PMC9512851 DOI: 10.1016/j.jbc.2022.102394] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 11/19/2022] Open
Abstract
Exosomes are small extracellular vesicles of ∼30 to 150 nm that are secreted by all cells, abundant in all biofluids, and play important roles in health and disease. However, details about the mechanism of exosome biogenesis are unclear. Here, we carried out a cargo-based analysis of exosome cargo protein biogenesis in which we identified the most highly enriched exosomal cargo proteins and then followed their biogenesis, trafficking, and exosomal secretion to test different hypotheses for how cells make exosomes. We show that exosome cargo proteins bud from cells (i) in exosome-sized vesicles regardless of whether they are localized to plasma or endosome membranes, (ii) ∼5-fold more efficiently when localized to the plasma membrane, (iii) ∼5-fold less efficiently when targeted to the endosome membrane, (iv) by a stochastic process that leads to ∼100-fold differences in their abundance from one exosome to another, and (v) independently of small GTPase Rab27a, the ESCRT complex–associated protein Alix, or the cargo protein CD63. Taken together, our results demonstrate that cells use a shared, stochastic mechanism to bud exosome cargoes along the spectrum of plasma and endosome membranes and far more efficiently from the plasma membrane than the endosome. Our observations also indicate that the pronounced variation in content between different exosome-sized vesicles is an inevitable consequence of a stochastic mechanism of small vesicle biogenesis, that the origin membrane of exosome-sized extracellular vesicles simply cannot be determined, and that most of what we currently know about exosomes has likely come from studies of plasma membrane-derived vesicles.
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Affiliation(s)
- Francis K Fordjour
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Chenxu Guo
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Yiwei Ai
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | | | - Stephen J Gould
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD, USA.
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10
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Dobre EG, Constantin C, Neagu M. Skin Cancer Research Goes Digital: Looking for Biomarkers within the Droplets. J Pers Med 2022; 12:jpm12071136. [PMID: 35887633 PMCID: PMC9323323 DOI: 10.3390/jpm12071136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 12/24/2022] Open
Abstract
Skin cancer, which includes the most frequent malignant non-melanoma carcinomas (basal cell carcinoma, BCC, and squamous cell carcinoma, SCC), along with the difficult to treat cutaneous melanoma (CM), pose important worldwide issues for the health care system. Despite the improved anti-cancer armamentarium and the latest scientific achievements, many skin cancer patients fail to respond to therapies, due to the remarkable heterogeneity of cutaneous tumors, calling for even more sophisticated biomarker discovery and patient monitoring approaches. Droplet digital polymerase chain reaction (ddPCR), a robust method for detecting and quantifying low-abundance nucleic acids, has recently emerged as a powerful technology for skin cancer analysis in tissue and liquid biopsies (LBs). The ddPCR method, being capable of analyzing various biological samples, has proved to be efficient in studying variations in gene sequences, including copy number variations (CNVs) and point mutations, DNA methylation, circulatory miRNome, and transcriptome dynamics. Moreover, ddPCR can be designed as a dynamic platform for individualized cancer detection and monitoring therapy efficacy. Here, we present the latest scientific studies applying ddPCR in dermato-oncology, highlighting the potential of this technology for skin cancer biomarker discovery and validation in the context of personalized medicine. The benefits and challenges associated with ddPCR implementation in the clinical setting, mainly when analyzing LBs, are also discussed.
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Affiliation(s)
- Elena-Georgiana Dobre
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91–95, 050095 Bucharest, Romania;
- Correspondence:
| | - Carolina Constantin
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania;
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Monica Neagu
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91–95, 050095 Bucharest, Romania;
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania;
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
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11
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Sjoqvist S, Otake K. A pilot study using proximity extension assay of cerebrospinal fluid and its extracellular vesicles identifies novel amyotrophic lateral sclerosis biomarker candidates. Biochem Biophys Res Commun 2022; 613:166-173. [PMID: 35567903 DOI: 10.1016/j.bbrc.2022.04.127] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/27/2022] [Indexed: 01/01/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder which is characterized by progressive degeneration of the motor system. Typically, the disease starts with focal weakness which spreads to involve most muscles and leads to death from respiratory failure within five years of diagnosis. Due to the heterogenic nature of the disease, diagnostics is complex, and it generally takes twelve months from symptom-onset to diagnosis. The discovery of novel biomarkers could lead to accelerated diagnosis, earlier start of treatment, improved patient-segmentation, and treatment follow-up as well as an increased insight into the pathology. Here, we analyzed cerebrospinal fluid (CSF) and CSF-derived extracellular vesicles (CSF-EVs) from ALS-patients and matched controls (n = 9 each) using the ultra-sensitive proximity extension assay (PEA), cardiovascular III-panel. On average, 84 and 61 proteins could be detected in CSF and CSF-EVs respectively. In CSF, three proteins were significantly upregulated in ALS-patients (Junctional Adhesion Molecule A Protein, Tumor necrosis factor receptor 2 and Chitinase 1) while myoglobin was down-regulated. In CSF-EVs, no significantly differentially expressed proteins were identified, but there was a trend for downregulation of Perlecan. To our knowledge, only CHIT1 has been previously described as a CSF-based biomarker candidate for ALS. By combining the four differentially expressed markers in CSF and support vector machine algorithm, all ALS patients and 8 of 9 controls were correctly classified. In conclusion, we here demonstrate the feasibility of using PEA of CSF and CSF-EVs for biomarker discovery and propose three de novo biomarker candidates for ALS, however, further studies are necessary to demonstrate clinical usability.
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Affiliation(s)
- Sebastian Sjoqvist
- Neuroscience Drug Discovery Unit, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan.
| | - Kentaro Otake
- Neuroscience Drug Discovery Unit, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
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Onoshima D, Baba Y. Cancer diagnosis and analysis devices based on multimolecular crowding. Chem Commun (Camb) 2021; 57:13655-13661. [PMID: 34854439 DOI: 10.1039/d1cc05556a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The study of the multimolecular crowding around cancer cells has opened up the possibility of developing new devices for cancer diagnosis and analysis through the measurement of intercellular communication related to cell proliferation and invasive metastasis associated with cancer malignancy. In particular, cells and extracellular vesicles that flow into the bloodstream contain metabolites and secreted products of the cancer microenvironment. These are positioned as targets for the development of new devices for the understanding and application of multimolecular crowding around cancer cells. Examples include the separation analysis of cancer cells in blood for the next generation of less invasive testing techniques, and mapping analysis using Raman scattering to detect cancer cells without staining. Another example is the evaluation of the relationship between exosomes and cancer traits for the exploration of new anti-cancer drugs, and the commercialization of exosome separation devices for ultra-early cancer diagnosis. The development of nanobiodevice engineering, which applies multimolecular crowding to conventional nanobioscience, is expected to contribute to the diagnosis and analysis of various diseases in the future.
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Affiliation(s)
- Daisuke Onoshima
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
| | - Yoshinobu Baba
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan. .,Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.,Institute of Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology (QST), Anagawa 4-9-1, Inage-ku, Chiba, 263-8555, Japan
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Qi F, Tan Y, Yao A, Yang X, He Y. Psoriasis to Psoriatic Arthritis: The Application of Proteomics Technologies. Front Med (Lausanne) 2021; 8:681172. [PMID: 34869404 PMCID: PMC8635007 DOI: 10.3389/fmed.2021.681172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Psoriatic disease (PsD) is a spectrum of diseases that affect both skin [cutaneous psoriasis (PsC)] and musculoskeletal features [psoriatic arthritis (PsA)]. A considerable number of patients with PsC have asymptomatic synovio-entheseal inflammations, and approximately one-third of those eventually progress to PsA with an enigmatic mechanism. Published studies have shown that early interventions to the very early-stage PsA would effectively prevent substantial bone destructions or deformities, suggesting an unmet goal for exploring early PsA biomarkers. The emergence of proteomics technologies brings a complete view of all involved proteins in PsA transitions, offers a unique chance to map all potential peptides, and allows a direct head-to-head comparison of interaction pathways in PsC and PsA. This review summarized the latest development of proteomics technologies, highlighted its application in PsA biomarker discovery, and discussed the possible clinical detectable PsA risk factors in patients with PsC.
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Affiliation(s)
- Fei Qi
- Department of Dermatology, Capital Medical University Affiliated Beijing Chaoyang Hospital, Beijing, China
| | - Yaqi Tan
- Department of Dermatology, Capital Medical University Affiliated Beijing Chaoyang Hospital, Beijing, China
| | - Amin Yao
- Department of Dermatology, Capital Medical University Affiliated Beijing Chaoyang Hospital, Beijing, China
| | - Xutong Yang
- Department of Dermatology, Capital Medical University Affiliated Beijing Chaoyang Hospital, Beijing, China
| | - Yanling He
- Department of Dermatology, Capital Medical University Affiliated Beijing Chaoyang Hospital, Beijing, China
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Shirejini SZ, Inci F. The Yin and Yang of exosome isolation methods: conventional practice, microfluidics, and commercial kits. Biotechnol Adv 2021; 54:107814. [PMID: 34389465 DOI: 10.1016/j.biotechadv.2021.107814] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 08/08/2021] [Accepted: 08/08/2021] [Indexed: 12/18/2022]
Abstract
Exosomes are a subset of extracellular vesicles released from various cells, and they can be found in different bodily fluids. Exosomes are used as biomarkers to diagnose many diseases and to monitor therapy efficiency as they represent the status and origin of the cell, which they are released from. Considering that they co-exist in bodily fluids with other types of particles, their isolation still remains challenging since conventional separation methods are time-consuming, user-dependent, and result in low isolation yield. This review summarizes the conventional strategies and microfluidic-based methods for exosome isolation along with their strengths and limitations. Microfluidic devices emerge as a promising approach to overcome the limitations of the conventional methods due to their inherent characteristics, such as the need for minute sample volume and rapid operation, in order to isolate exosomes with a high yield and a high purity in a short amount of time, which make them unprecedented tools for molecular biology and clinical applications. This review elaborates on the existing microfluidic-based exosome isolation methods and denotes their benefits and drawbacks. Herein, we also introduce various commercially available platforms and kits for exosome isolation along with their working principles.
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Affiliation(s)
- Saeedreza Zeibi Shirejini
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Fatih Inci
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey; Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey.
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